/**
 * PHOSIDE: PHosphorylation Site IDentification Engine.
 * Copyright 2009 Digital Biology Lab, University of Missouri.
 * This library is free software; you can redistribute it and/or modify it under
 * the terms of the GNU General Public License as published by the Free Software
 * Foundation; either version 3 of the License, or (at your option) any later
 * version. <p/> This library is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the License for more
 * details.
 */

package phoside.io.fasta;

import java.io.IOException;

import phoside.PhosphoProteins;

import phoside.io.fasta.parser.HeaderRule;
import phoside.io.fasta.parser.DefaultPhosphoSequenceParser;


/**
 *
 * @author gjj
 */
public class PhosphoReaderFromFastaWithSitesInSequence
                        extends FastaProteinsReaderFromFile {

    public PhosphoReaderFromFastaWithSitesInSequence(final String fasta,
            final PhosphoProteins phosphoData, final HeaderRule headerRule)
            throws IOException {
        this(fasta, phosphoData, headerRule, new DefaultPhosphoSequenceParser("#"));
    }

    public PhosphoReaderFromFastaWithSitesInSequence(final String fasta,
            final PhosphoProteins phosphoData, final HeaderRule headerRule,
            final DefaultPhosphoSequenceParser sequenceParser)
            throws IOException {
        super(fasta,new PhosphoReaderFastaVisitorWithSitesInSequence(phosphoData,
                headerRule, sequenceParser));
    }

}
